chr12-109356932-A-G

Variant names:

• chr12-109356932-A-G
• rs9332412
• NM_001101421.4:c.12+8960A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001101421.4(MYO1H):​c.12+8960A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 152,006 control chromosomes in the GnomAD database, including 17,944 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.48 (17944 hom., cov: 31)
• Consequence: MYO1H NM_001101421.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 6 publications found

Genes affected

MYO1H (HGNC:13879): (myosin IH) Predicted to enable actin filament binding activity and microfilament motor activity. Predicted to be involved in actin filament organization and vesicle transport along actin filament. Predicted to be part of myosin complex. Predicted to be active in several cellular components, including actin cytoskeleton; microvillus; and vesicle. [provided by Alliance of Genome Resources, Apr 2022]

LINC01486 (HGNC:51137): (long intergenic non-protein coding RNA 1486)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO1H	NM_001101421.4	c.12+8960A>G		intron_variant	Intron 1 of 31	ENST00000310903.10	NP_001094891.4
LINC01486	NR_120462.1	n.363+200T>C		intron_variant	Intron 2 of 2
MYO1H	XM_011538223.3	c.-36-31751A>G		intron_variant	Intron 2 of 33		XP_011536525.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO1H	ENST00000310903.10	c.12+8960A>G		intron_variant	Intron 1 of 31	5	NM_001101421.4	ENSP00000439182.2
LINC01486	ENST00000538041.2	n.382+200T>C		intron_variant	Intron 2 of 2	2
LINC01486	ENST00000724587.1	n.219+200T>C		intron_variant	Intron 2 of 2
LINC01486	ENST00000724588.1	n.272+2329T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72532 AN: 151888 Hom.: 17907 Cov.: 31

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.496

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.478 AC: 72613 AN: 152006 Hom.: 17944 Cov.: 31 AF XY: 0.471 AC XY: 34970 AN XY: 74280

African (AFR) AF: 0.580 AC: 24011 AN: 41434

American (AMR) AF: 0.541 AC: 8256 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1737 AN: 3468

East Asian (EAS) AF: 0.358 AC: 1855 AN: 5176

South Asian (SAS) AF: 0.348 AC: 1676 AN: 4818

European-Finnish (FIN) AF: 0.327 AC: 3456 AN: 10564

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.441 AC: 29969 AN: 67964

Other (OTH) AF: 0.491 AC: 1039 AN: 2114

Alfa AF: 0.458 Hom.: 2003

Bravo AF: 0.504

Asia WGS AF: 0.330 AC: 1148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.67
PhyloP100		-0.18
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9332412; hg19: chr12-109794737; COSMIC: COSV60448773;